I don't know if the pain you're having is related, but I had the exact same pain when I had hydronephrosis during my pregnancy. My ureters were blocked by the baby/uterus. It was misdiagnosed as a few things (stones, etc) before an ultrasound showed what was going on.

Dark stool like you're describing may mean that you're bleeding higher in your digestive tract. Since it's black, the blood is old, which is concerning. I would ask your doc for further testing on both issues!